Beispiel #1
0
 void createMask(ImagePlus imp) {
   Roi roi = imp.getRoi();
   boolean useInvertingLut = Prefs.useInvertingLut;
   Prefs.useInvertingLut = false;
   if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT)) {
     createMaskFromThreshold(imp);
     Prefs.useInvertingLut = useInvertingLut;
     return;
   }
   ImagePlus maskImp = null;
   Frame frame = WindowManager.getFrame("Mask");
   if (frame != null && (frame instanceof ImageWindow))
     maskImp = ((ImageWindow) frame).getImagePlus();
   if (maskImp == null) {
     ImageProcessor ip = new ByteProcessor(imp.getWidth(), imp.getHeight());
     if (!Prefs.blackBackground) ip.invertLut();
     maskImp = new ImagePlus("Mask", ip);
     maskImp.show();
   }
   ImageProcessor ip = maskImp.getProcessor();
   ip.setRoi(roi);
   ip.setValue(255);
   ip.fill(ip.getMask());
   maskImp.updateAndDraw();
   Prefs.useInvertingLut = useInvertingLut;
 }
Beispiel #2
0
 void createEllipse(ImagePlus imp) {
   IJ.showStatus("Fitting ellipse");
   Roi roi = imp.getRoi();
   if (roi == null) {
     noRoi("Fit Ellipse");
     return;
   }
   if (roi.isLine()) {
     IJ.error("Fit Ellipse", "\"Fit Ellipse\" does not work with line selections");
     return;
   }
   ImageProcessor ip = imp.getProcessor();
   ip.setRoi(roi);
   int options = Measurements.CENTROID + Measurements.ELLIPSE;
   ImageStatistics stats = ImageStatistics.getStatistics(ip, options, null);
   double dx = stats.major * Math.cos(stats.angle / 180.0 * Math.PI) / 2.0;
   double dy = -stats.major * Math.sin(stats.angle / 180.0 * Math.PI) / 2.0;
   double x1 = stats.xCentroid - dx;
   double x2 = stats.xCentroid + dx;
   double y1 = stats.yCentroid - dy;
   double y2 = stats.yCentroid + dy;
   double aspectRatio = stats.minor / stats.major;
   imp.killRoi();
   imp.setRoi(new EllipseRoi(x1, y1, x2, y2, aspectRatio));
 }
 boolean eraseOutsideRoi(ImageProcessor ip, Rectangle r, ImageProcessor mask) {
   int width = ip.getWidth();
   int height = ip.getHeight();
   ip.setRoi(r);
   if (excludeEdgeParticles && polygon != null) {
     ImageStatistics stats = ImageStatistics.getStatistics(ip, MIN_MAX, null);
     if (fillColor >= stats.min && fillColor <= stats.max) {
       double replaceColor = level1 - 1.0;
       if (replaceColor < 0.0 || replaceColor == fillColor) {
         replaceColor = level2 + 1.0;
         int maxColor = imageType == BYTE ? 255 : 65535;
         if (replaceColor > maxColor || replaceColor == fillColor) {
           IJ.error("Particle Analyzer", "Unable to remove edge particles");
           return false;
         }
       }
       for (int y = minY; y < maxY; y++) {
         for (int x = minX; x < maxX; x++) {
           int v = ip.getPixel(x, y);
           if (v == fillColor) ip.putPixel(x, y, (int) replaceColor);
         }
       }
     }
   }
   ip.setValue(fillColor);
   if (mask != null) {
     mask = mask.duplicate();
     mask.invert();
     ip.fill(mask);
   }
   ip.setRoi(0, 0, r.x, height);
   ip.fill();
   ip.setRoi(r.x, 0, r.width, r.y);
   ip.fill();
   ip.setRoi(r.x, r.y + r.height, r.width, height - (r.y + r.height));
   ip.fill();
   ip.setRoi(r.x + r.width, 0, width - (r.x + r.width), height);
   ip.fill();
   ip.resetRoi();
   // IJ.log("erase: "+fillColor+"	"+level1+"	"+level2+"	"+excludeEdgeParticles);
   // (new ImagePlus("ip2", ip.duplicate())).show();
   return true;
 }
Beispiel #4
0
 void createNewStack(ImagePlus imp, ImageProcessor ip) {
   int nSlices = imp.getStackSize();
   int w = imp.getWidth(), h = imp.getHeight();
   ImagePlus imp2 = imp.createImagePlus();
   Rectangle r = ip.getRoi();
   boolean crop = r.width != imp.getWidth() || r.height != imp.getHeight();
   ImageStack stack1 = imp.getStack();
   ImageStack stack2 = new ImageStack(newWidth, newHeight);
   ImageProcessor ip1, ip2;
   int method = interpolationMethod;
   if (w == 1 || h == 1) method = ImageProcessor.NONE;
   for (int i = 1; i <= nSlices; i++) {
     IJ.showStatus("Scale: " + i + "/" + nSlices);
     ip1 = stack1.getProcessor(i);
     String label = stack1.getSliceLabel(i);
     if (crop) {
       ip1.setRoi(r);
       ip1 = ip1.crop();
     }
     ip1.setInterpolationMethod(method);
     ip2 = ip1.resize(newWidth, newHeight, averageWhenDownsizing);
     if (ip2 != null) stack2.addSlice(label, ip2);
     IJ.showProgress(i, nSlices);
   }
   imp2.setStack(title, stack2);
   Calibration cal = imp2.getCalibration();
   if (cal.scaled()) {
     cal.pixelWidth *= 1.0 / xscale;
     cal.pixelHeight *= 1.0 / yscale;
   }
   IJ.showProgress(1.0);
   int[] dim = imp.getDimensions();
   imp2.setDimensions(dim[2], dim[3], dim[4]);
   if (imp.isComposite()) {
     imp2 = new CompositeImage(imp2, ((CompositeImage) imp).getMode());
     ((CompositeImage) imp2).copyLuts(imp);
   }
   if (imp.isHyperStack()) imp2.setOpenAsHyperStack(true);
   if (newDepth > 0 && newDepth != oldDepth)
     imp2 = (new Resizer()).zScale(imp2, newDepth, interpolationMethod);
   if (imp2 != null) {
     imp2.show();
     imp2.changes = true;
   }
 }
 private String addMean(int column, String line, int start) {
   if (start == -1) {
     line += "\tNaN";
     summaryHdr += "\t" + ResultsTable.getDefaultHeading(column);
   } else {
     float[] c = column >= 0 ? rt.getColumn(column) : null;
     if (c != null) {
       ImageProcessor ip = new FloatProcessor(c.length, 1, c, null);
       if (ip == null) return line;
       ip.setRoi(start, 0, ip.getWidth() - start, 1);
       ip = ip.crop();
       ImageStatistics stats = new FloatStatistics(ip);
       if (stats == null) return line;
       line += n(stats.mean);
     } else line += "\tNaN";
     summaryHdr += "\t" + rt.getColumnHeading(column);
   }
   return line;
 }
Beispiel #6
0
 void createNewStack(ImagePlus imp, ImageProcessor ip) {
   Rectangle r = ip.getRoi();
   boolean crop = r.width != imp.getWidth() || r.height != imp.getHeight();
   int nSlices = imp.getStackSize();
   ImageStack stack1 = imp.getStack();
   ImageStack stack2 = new ImageStack(newWidth, newHeight);
   ImageProcessor ip1, ip2;
   boolean interp = interpolate;
   if (imp.getWidth() == 1 || imp.getHeight() == 1) interp = false;
   for (int i = 1; i <= nSlices; i++) {
     IJ.showStatus("Scale: " + i + "/" + nSlices);
     ip1 = stack1.getProcessor(i);
     String label = stack1.getSliceLabel(i);
     if (crop) {
       ip1.setRoi(r);
       ip1 = ip1.crop();
     }
     ip1.setInterpolate(interp);
     ip2 = ip1.resize(newWidth, newHeight);
     if (ip2 != null) stack2.addSlice(label, ip2);
     IJ.showProgress(i, nSlices);
   }
   ImagePlus imp2 = imp.createImagePlus();
   imp2.setStack(title, stack2);
   Calibration cal = imp2.getCalibration();
   if (cal.scaled()) {
     cal.pixelWidth *= 1.0 / xscale;
     cal.pixelHeight *= 1.0 / yscale;
   }
   int[] dim = imp.getDimensions();
   imp2.setDimensions(dim[2], dim[3], dim[4]);
   IJ.showProgress(1.0);
   if (imp.isComposite()) {
     imp2 = new CompositeImage(imp2, 0);
     ((CompositeImage) imp2).copyLuts(imp);
   }
   if (imp.isHyperStack()) imp2.setOpenAsHyperStack(true);
   imp2.show();
   imp2.changes = true;
 }
Beispiel #7
0
 void createMask(ImagePlus imp) {
   Roi roi = imp.getRoi();
   boolean useInvertingLut = Prefs.useInvertingLut;
   Prefs.useInvertingLut = false;
   boolean selectAll =
       roi != null
           && roi.getType() == Roi.RECTANGLE
           && roi.getBounds().width == imp.getWidth()
           && roi.getBounds().height == imp.getHeight()
           && imp.isThreshold();
   if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT) || selectAll) {
     createMaskFromThreshold(imp);
     Prefs.useInvertingLut = useInvertingLut;
     return;
   }
   ImagePlus maskImp = null;
   Frame frame = WindowManager.getFrame("Mask");
   if (frame != null && (frame instanceof ImageWindow))
     maskImp = ((ImageWindow) frame).getImagePlus();
   if (maskImp == null) {
     ImageProcessor ip = new ByteProcessor(imp.getWidth(), imp.getHeight());
     if (!Prefs.blackBackground) ip.invertLut();
     maskImp = new ImagePlus("Mask", ip);
     maskImp.show();
   }
   ImageProcessor ip = maskImp.getProcessor();
   ip.setRoi(roi);
   ip.setValue(255);
   ip.fill(ip.getMask());
   Calibration cal = imp.getCalibration();
   if (cal.scaled()) {
     Calibration cal2 = maskImp.getCalibration();
     cal2.pixelWidth = cal.pixelWidth;
     cal2.pixelHeight = cal.pixelHeight;
     cal2.setUnit(cal.getUnit());
   }
   maskImp.updateAndRepaintWindow();
   Prefs.useInvertingLut = useInvertingLut;
 }
Beispiel #8
0
  /*
  if selection is closed shape, create a circle with the same area and centroid, otherwise use<br>
  the Pratt method to fit a circle to the points that define the line or multi-point selection.<br>
  Reference: Pratt V., Direct least-squares fitting of algebraic surfaces", Computer Graphics, Vol. 21, pages 145-152 (1987).<br>
  Original code: Nikolai Chernov's MATLAB script for Newton-based Pratt fit.<br>
  (http://www.math.uab.edu/~chernov/cl/MATLABcircle.html)<br>
  Java version: https://github.com/mdoube/BoneJ/blob/master/src/org/doube/geometry/FitCircle.java<br>
  @authors Nikolai Chernov, Michael Doube, Ved Sharma
  */
  void fitCircle(ImagePlus imp) {
    Roi roi = imp.getRoi();
    if (roi == null) {
      noRoi("Fit Circle");
      return;
    }

    if (roi.isArea()) { // create circle with the same area and centroid
      ImageProcessor ip = imp.getProcessor();
      ip.setRoi(roi);
      ImageStatistics stats =
          ImageStatistics.getStatistics(ip, Measurements.AREA + Measurements.CENTROID, null);
      double r = Math.sqrt(stats.pixelCount / Math.PI);
      imp.killRoi();
      int d = (int) Math.round(2.0 * r);
      IJ.makeOval(
          (int) Math.round(stats.xCentroid - r), (int) Math.round(stats.yCentroid - r), d, d);
      return;
    }

    Polygon poly = roi.getPolygon();
    int n = poly.npoints;
    int[] x = poly.xpoints;
    int[] y = poly.ypoints;
    if (n < 3) {
      IJ.error("Fit Circle", "At least 3 points are required to fit a circle.");
      return;
    }

    // calculate point centroid
    double sumx = 0, sumy = 0;
    for (int i = 0; i < n; i++) {
      sumx = sumx + poly.xpoints[i];
      sumy = sumy + poly.ypoints[i];
    }
    double meanx = sumx / n;
    double meany = sumy / n;

    // calculate moments
    double[] X = new double[n], Y = new double[n];
    double Mxx = 0, Myy = 0, Mxy = 0, Mxz = 0, Myz = 0, Mzz = 0;
    for (int i = 0; i < n; i++) {
      X[i] = x[i] - meanx;
      Y[i] = y[i] - meany;
      double Zi = X[i] * X[i] + Y[i] * Y[i];
      Mxy = Mxy + X[i] * Y[i];
      Mxx = Mxx + X[i] * X[i];
      Myy = Myy + Y[i] * Y[i];
      Mxz = Mxz + X[i] * Zi;
      Myz = Myz + Y[i] * Zi;
      Mzz = Mzz + Zi * Zi;
    }
    Mxx = Mxx / n;
    Myy = Myy / n;
    Mxy = Mxy / n;
    Mxz = Mxz / n;
    Myz = Myz / n;
    Mzz = Mzz / n;

    // calculate the coefficients of the characteristic polynomial
    double Mz = Mxx + Myy;
    double Cov_xy = Mxx * Myy - Mxy * Mxy;
    double Mxz2 = Mxz * Mxz;
    double Myz2 = Myz * Myz;
    double A2 = 4 * Cov_xy - 3 * Mz * Mz - Mzz;
    double A1 = Mzz * Mz + 4 * Cov_xy * Mz - Mxz2 - Myz2 - Mz * Mz * Mz;
    double A0 = Mxz2 * Myy + Myz2 * Mxx - Mzz * Cov_xy - 2 * Mxz * Myz * Mxy + Mz * Mz * Cov_xy;
    double A22 = A2 + A2;
    double epsilon = 1e-12;
    double ynew = 1e+20;
    int IterMax = 20;
    double xnew = 0;
    int iterations = 0;

    // Newton's method starting at x=0
    for (int iter = 1; iter <= IterMax; iter++) {
      iterations = iter;
      double yold = ynew;
      ynew = A0 + xnew * (A1 + xnew * (A2 + 4. * xnew * xnew));
      if (Math.abs(ynew) > Math.abs(yold)) {
        if (IJ.debugMode) IJ.log("Fit Circle: wrong direction: |ynew| > |yold|");
        xnew = 0;
        break;
      }
      double Dy = A1 + xnew * (A22 + 16 * xnew * xnew);
      double xold = xnew;
      xnew = xold - ynew / Dy;
      if (Math.abs((xnew - xold) / xnew) < epsilon) break;
      if (iter >= IterMax) {
        if (IJ.debugMode) IJ.log("Fit Circle: will not converge");
        xnew = 0;
      }
      if (xnew < 0) {
        if (IJ.debugMode) IJ.log("Fit Circle: negative root:  x = " + xnew);
        xnew = 0;
      }
    }
    if (IJ.debugMode)
      IJ.log("Fit Circle: n=" + n + ", xnew=" + IJ.d2s(xnew, 2) + ", iterations=" + iterations);

    // calculate the circle parameters
    double DET = xnew * xnew - xnew * Mz + Cov_xy;
    double CenterX = (Mxz * (Myy - xnew) - Myz * Mxy) / (2 * DET);
    double CenterY = (Myz * (Mxx - xnew) - Mxz * Mxy) / (2 * DET);
    double radius = Math.sqrt(CenterX * CenterX + CenterY * CenterY + Mz + 2 * xnew);
    if (Double.isNaN(radius)) {
      IJ.error("Fit Circle", "Points are collinear.");
      return;
    }
    CenterX = CenterX + meanx;
    CenterY = CenterY + meany;
    imp.killRoi();
    IJ.makeOval(
        (int) Math.round(CenterX - radius),
        (int) Math.round(CenterY - radius),
        (int) Math.round(2 * radius),
        (int) Math.round(2 * radius));
  }
  public void build_bricks() {

    ImagePlus imp;
    ImagePlus orgimp;
    ImageStack stack;
    FileInfo finfo;

    if (lvImgTitle.isEmpty()) return;
    orgimp = WindowManager.getImage(lvImgTitle.get(0));
    imp = orgimp;

    finfo = imp.getFileInfo();
    if (finfo == null) return;

    int[] dims = imp.getDimensions();
    int imageW = dims[0];
    int imageH = dims[1];
    int nCh = dims[2];
    int imageD = dims[3];
    int nFrame = dims[4];
    int bdepth = imp.getBitDepth();
    double xspc = finfo.pixelWidth;
    double yspc = finfo.pixelHeight;
    double zspc = finfo.pixelDepth;
    double z_aspect = Math.max(xspc, yspc) / zspc;

    int orgW = imageW;
    int orgH = imageH;
    int orgD = imageD;
    double orgxspc = xspc;
    double orgyspc = yspc;
    double orgzspc = zspc;

    lv = lvImgTitle.size();
    if (filetype == "JPEG") {
      for (int l = 0; l < lv; l++) {
        if (WindowManager.getImage(lvImgTitle.get(l)).getBitDepth() != 8) {
          IJ.error("A SOURCE IMAGE MUST BE 8BIT GLAYSCALE");
          return;
        }
      }
    }

    // calculate levels
    /*		int baseXY = 256;
    		int baseZ = 256;

    		if (z_aspect < 0.5) baseZ = 128;
    		if (z_aspect > 2.0) baseXY = 128;
    		if (z_aspect >= 0.5 && z_aspect < 1.0) baseZ = (int)(baseZ*z_aspect);
    		if (z_aspect > 1.0 && z_aspect <= 2.0) baseXY = (int)(baseXY/z_aspect);

    		IJ.log("Z_aspect: " + z_aspect);
    		IJ.log("BaseXY: " + baseXY);
    		IJ.log("BaseZ: " + baseZ);
    */

    int baseXY = 256;
    int baseZ = 128;
    int dbXY = Math.max(orgW, orgH) / baseXY;
    if (Math.max(orgW, orgH) % baseXY > 0) dbXY *= 2;
    int dbZ = orgD / baseZ;
    if (orgD % baseZ > 0) dbZ *= 2;
    lv = Math.max(log2(dbXY), log2(dbZ)) + 1;

    int ww = orgW;
    int hh = orgH;
    int dd = orgD;
    for (int l = 0; l < lv; l++) {
      int bwnum = ww / baseXY;
      if (ww % baseXY > 0) bwnum++;
      int bhnum = hh / baseXY;
      if (hh % baseXY > 0) bhnum++;
      int bdnum = dd / baseZ;
      if (dd % baseZ > 0) bdnum++;

      if (bwnum % 2 == 0) bwnum++;
      if (bhnum % 2 == 0) bhnum++;
      if (bdnum % 2 == 0) bdnum++;

      int bw = (bwnum <= 1) ? ww : ww / bwnum + 1 + (ww % bwnum > 0 ? 1 : 0);
      int bh = (bhnum <= 1) ? hh : hh / bhnum + 1 + (hh % bhnum > 0 ? 1 : 0);
      int bd = (bdnum <= 1) ? dd : dd / bdnum + 1 + (dd % bdnum > 0 ? 1 : 0);

      bwlist.add(bw);
      bhlist.add(bh);
      bdlist.add(bd);

      IJ.log("LEVEL: " + l);
      IJ.log("  width: " + ww);
      IJ.log("  hight: " + hh);
      IJ.log("  depth: " + dd);
      IJ.log("  bw: " + bw);
      IJ.log("  bh: " + bh);
      IJ.log("  bd: " + bd);

      int xyl2 = Math.max(ww, hh) / baseXY;
      if (Math.max(ww, hh) % baseXY > 0) xyl2 *= 2;
      if (lv - 1 - log2(xyl2) <= l) {
        ww /= 2;
        hh /= 2;
      }
      IJ.log("  xyl2: " + (lv - 1 - log2(xyl2)));

      int zl2 = dd / baseZ;
      if (dd % baseZ > 0) zl2 *= 2;
      if (lv - 1 - log2(zl2) <= l) dd /= 2;
      IJ.log("  zl2: " + (lv - 1 - log2(zl2)));

      if (l < lv - 1) {
        lvImgTitle.add(lvImgTitle.get(0) + "_level" + (l + 1));
        IJ.selectWindow(lvImgTitle.get(0));
        IJ.run(
            "Scale...",
            "x=- y=- z=- width="
                + ww
                + " height="
                + hh
                + " depth="
                + dd
                + " interpolation=Bicubic average process create title="
                + lvImgTitle.get(l + 1));
      }
    }

    for (int l = 0; l < lv; l++) {
      IJ.log(lvImgTitle.get(l));
    }

    Document doc = newXMLDocument();
    Element root = doc.createElement("BRK");
    root.setAttribute("version", "1.0");
    root.setAttribute("nLevel", String.valueOf(lv));
    root.setAttribute("nChannel", String.valueOf(nCh));
    root.setAttribute("nFrame", String.valueOf(nFrame));
    doc.appendChild(root);

    for (int l = 0; l < lv; l++) {
      IJ.showProgress(0.0);

      int[] dims2 = imp.getDimensions();
      IJ.log(
          "W: "
              + String.valueOf(dims2[0])
              + " H: "
              + String.valueOf(dims2[1])
              + " C: "
              + String.valueOf(dims2[2])
              + " D: "
              + String.valueOf(dims2[3])
              + " T: "
              + String.valueOf(dims2[4])
              + " b: "
              + String.valueOf(bdepth));

      bw = bwlist.get(l).intValue();
      bh = bhlist.get(l).intValue();
      bd = bdlist.get(l).intValue();

      boolean force_pow2 = false;
      /*			if(IsPowerOf2(bw) && IsPowerOf2(bh) && IsPowerOf2(bd)) force_pow2 = true;

      			if(force_pow2){
      				//force pow2
      				if(Pow2(bw) > bw) bw = Pow2(bw)/2;
      				if(Pow2(bh) > bh) bh = Pow2(bh)/2;
      				if(Pow2(bd) > bd) bd = Pow2(bd)/2;
      			}

      			if(bw > imageW) bw = (Pow2(imageW) == imageW) ? imageW : Pow2(imageW)/2;
      			if(bh > imageH) bh = (Pow2(imageH) == imageH) ? imageH : Pow2(imageH)/2;
      			if(bd > imageD) bd = (Pow2(imageD) == imageD) ? imageD : Pow2(imageD)/2;

      */
      if (bw > imageW) bw = imageW;
      if (bh > imageH) bh = imageH;
      if (bd > imageD) bd = imageD;

      if (bw <= 1 || bh <= 1 || bd <= 1) break;

      if (filetype == "JPEG" && (bw < 8 || bh < 8)) break;

      Element lvnode = doc.createElement("Level");
      lvnode.setAttribute("lv", String.valueOf(l));
      lvnode.setAttribute("imageW", String.valueOf(imageW));
      lvnode.setAttribute("imageH", String.valueOf(imageH));
      lvnode.setAttribute("imageD", String.valueOf(imageD));
      lvnode.setAttribute("xspc", String.valueOf(xspc));
      lvnode.setAttribute("yspc", String.valueOf(yspc));
      lvnode.setAttribute("zspc", String.valueOf(zspc));
      lvnode.setAttribute("bitDepth", String.valueOf(bdepth));
      root.appendChild(lvnode);

      Element brksnode = doc.createElement("Bricks");
      brksnode.setAttribute("brick_baseW", String.valueOf(bw));
      brksnode.setAttribute("brick_baseH", String.valueOf(bh));
      brksnode.setAttribute("brick_baseD", String.valueOf(bd));
      lvnode.appendChild(brksnode);

      ArrayList<Brick> bricks = new ArrayList<Brick>();
      int mw, mh, md, mw2, mh2, md2;
      double tx0, ty0, tz0, tx1, ty1, tz1;
      double bx0, by0, bz0, bx1, by1, bz1;
      for (int k = 0; k < imageD; k += bd) {
        if (k > 0) k--;
        for (int j = 0; j < imageH; j += bh) {
          if (j > 0) j--;
          for (int i = 0; i < imageW; i += bw) {
            if (i > 0) i--;
            mw = Math.min(bw, imageW - i);
            mh = Math.min(bh, imageH - j);
            md = Math.min(bd, imageD - k);

            if (force_pow2) {
              mw2 = Pow2(mw);
              mh2 = Pow2(mh);
              md2 = Pow2(md);
            } else {
              mw2 = mw;
              mh2 = mh;
              md2 = md;
            }

            if (filetype == "JPEG") {
              if (mw2 < 8) mw2 = 8;
              if (mh2 < 8) mh2 = 8;
            }

            tx0 = i == 0 ? 0.0d : ((mw2 - mw + 0.5d) / mw2);
            ty0 = j == 0 ? 0.0d : ((mh2 - mh + 0.5d) / mh2);
            tz0 = k == 0 ? 0.0d : ((md2 - md + 0.5d) / md2);

            tx1 = 1.0d - 0.5d / mw2;
            if (mw < bw) tx1 = 1.0d;
            if (imageW - i == bw) tx1 = 1.0d;

            ty1 = 1.0d - 0.5d / mh2;
            if (mh < bh) ty1 = 1.0d;
            if (imageH - j == bh) ty1 = 1.0d;

            tz1 = 1.0d - 0.5d / md2;
            if (md < bd) tz1 = 1.0d;
            if (imageD - k == bd) tz1 = 1.0d;

            bx0 = i == 0 ? 0.0d : (i + 0.5d) / (double) imageW;
            by0 = j == 0 ? 0.0d : (j + 0.5d) / (double) imageH;
            bz0 = k == 0 ? 0.0d : (k + 0.5d) / (double) imageD;

            bx1 = Math.min((i + bw - 0.5d) / (double) imageW, 1.0d);
            if (imageW - i == bw) bx1 = 1.0d;

            by1 = Math.min((j + bh - 0.5d) / (double) imageH, 1.0d);
            if (imageH - j == bh) by1 = 1.0d;

            bz1 = Math.min((k + bd - 0.5d) / (double) imageD, 1.0d);
            if (imageD - k == bd) bz1 = 1.0d;

            int x, y, z;
            x = i - (mw2 - mw);
            y = j - (mh2 - mh);
            z = k - (md2 - md);
            bricks.add(
                new Brick(
                    x, y, z, mw2, mh2, md2, 0, 0, tx0, ty0, tz0, tx1, ty1, tz1, bx0, by0, bz0, bx1,
                    by1, bz1));
          }
        }
      }

      Element fsnode = doc.createElement("Files");
      lvnode.appendChild(fsnode);

      stack = imp.getStack();

      int totalbricknum = nFrame * nCh * bricks.size();
      int curbricknum = 0;
      for (int f = 0; f < nFrame; f++) {
        for (int ch = 0; ch < nCh; ch++) {
          int sizelimit = bdsizelimit * 1024 * 1024;
          int bytecount = 0;
          int filecount = 0;
          int pd_bufsize = Math.max(sizelimit, bw * bh * bd * bdepth / 8);
          byte[] packed_data = new byte[pd_bufsize];
          String base_dataname =
              basename
                  + "_Lv"
                  + String.valueOf(l)
                  + "_Ch"
                  + String.valueOf(ch)
                  + "_Fr"
                  + String.valueOf(f);
          String current_dataname = base_dataname + "_data" + filecount;

          Brick b_first = bricks.get(0);
          if (b_first.z_ != 0) IJ.log("warning");
          int st_z = b_first.z_;
          int ed_z = b_first.z_ + b_first.d_;
          LinkedList<ImageProcessor> iplist = new LinkedList<ImageProcessor>();
          for (int s = st_z; s < ed_z; s++)
            iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));

          //					ImagePlus test;
          //					ImageStack tsst;
          //					test = NewImage.createByteImage("test", imageW, imageH, imageD,
          // NewImage.FILL_BLACK);
          //					tsst = test.getStack();
          for (int i = 0; i < bricks.size(); i++) {
            Brick b = bricks.get(i);

            if (ed_z > b.z_ || st_z < b.z_ + b.d_) {
              if (b.z_ > st_z) {
                for (int s = 0; s < b.z_ - st_z; s++) iplist.pollFirst();
                st_z = b.z_;
              } else if (b.z_ < st_z) {
                IJ.log("warning");
                for (int s = st_z - 1; s > b.z_; s--)
                  iplist.addFirst(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
                st_z = b.z_;
              }

              if (b.z_ + b.d_ > ed_z) {
                for (int s = ed_z; s < b.z_ + b.d_; s++)
                  iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
                ed_z = b.z_ + b.d_;
              } else if (b.z_ + b.d_ < ed_z) {
                IJ.log("warning");
                for (int s = 0; s < ed_z - (b.z_ + b.d_); s++) iplist.pollLast();
                ed_z = b.z_ + b.d_;
              }
            } else {
              IJ.log("warning");
              iplist.clear();
              st_z = b.z_;
              ed_z = b.z_ + b.d_;
              for (int s = st_z; s < ed_z; s++)
                iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
            }

            if (iplist.size() != b.d_) {
              IJ.log("Stack Error");
              return;
            }

            //						int zz = st_z;

            int bsize = 0;
            byte[] bdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
            Iterator<ImageProcessor> ipite = iplist.iterator();
            while (ipite.hasNext()) {

              //							ImageProcessor tsip = tsst.getProcessor(zz+1);

              ImageProcessor ip = ipite.next();
              ip.setRoi(b.x_, b.y_, b.w_, b.h_);
              if (bdepth == 8) {
                byte[] data = (byte[]) ip.crop().getPixels();
                System.arraycopy(data, 0, bdata, bsize, data.length);
                bsize += data.length;
              } else if (bdepth == 16) {
                ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
                buffer.order(ByteOrder.LITTLE_ENDIAN);
                short[] data = (short[]) ip.crop().getPixels();
                for (short e : data) buffer.putShort(e);
                System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
                bsize += buffer.array().length;
              } else if (bdepth == 32) {
                ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
                buffer.order(ByteOrder.LITTLE_ENDIAN);
                float[] data = (float[]) ip.crop().getPixels();
                for (float e : data) buffer.putFloat(e);
                System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
                bsize += buffer.array().length;
              }
            }

            String filename =
                basename
                    + "_Lv"
                    + String.valueOf(l)
                    + "_Ch"
                    + String.valueOf(ch)
                    + "_Fr"
                    + String.valueOf(f)
                    + "_ID"
                    + String.valueOf(i);

            int offset = bytecount;
            int datasize = bdata.length;

            if (filetype == "RAW") {
              int dummy = -1;
              // do nothing
            }
            if (filetype == "JPEG" && bdepth == 8) {
              try {
                DataBufferByte db = new DataBufferByte(bdata, datasize);
                Raster raster = Raster.createPackedRaster(db, b.w_, b.h_ * b.d_, 8, null);
                BufferedImage img =
                    new BufferedImage(b.w_, b.h_ * b.d_, BufferedImage.TYPE_BYTE_GRAY);
                img.setData(raster);
                ByteArrayOutputStream baos = new ByteArrayOutputStream();
                ImageOutputStream ios = ImageIO.createImageOutputStream(baos);
                String format = "jpg";
                Iterator<javax.imageio.ImageWriter> iter =
                    ImageIO.getImageWritersByFormatName("jpeg");
                javax.imageio.ImageWriter writer = iter.next();
                ImageWriteParam iwp = writer.getDefaultWriteParam();
                iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
                iwp.setCompressionQuality((float) jpeg_quality * 0.01f);
                writer.setOutput(ios);
                writer.write(null, new IIOImage(img, null, null), iwp);
                // ImageIO.write(img, format, baos);
                bdata = baos.toByteArray();
                datasize = bdata.length;
              } catch (IOException e) {
                e.printStackTrace();
                return;
              }
            }
            if (filetype == "ZLIB") {
              byte[] tmpdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
              Deflater compresser = new Deflater();
              compresser.setInput(bdata);
              compresser.setLevel(Deflater.DEFAULT_COMPRESSION);
              compresser.setStrategy(Deflater.DEFAULT_STRATEGY);
              compresser.finish();
              datasize = compresser.deflate(tmpdata);
              bdata = tmpdata;
              compresser.end();
            }

            if (bytecount + datasize > sizelimit && bytecount > 0) {
              BufferedOutputStream fis = null;
              try {
                File file = new File(directory + current_dataname);
                fis = new BufferedOutputStream(new FileOutputStream(file));
                fis.write(packed_data, 0, bytecount);
              } catch (IOException e) {
                e.printStackTrace();
                return;
              } finally {
                try {
                  if (fis != null) fis.close();
                } catch (IOException e) {
                  e.printStackTrace();
                  return;
                }
              }
              filecount++;
              current_dataname = base_dataname + "_data" + filecount;
              bytecount = 0;
              offset = 0;
              System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
              bytecount += datasize;
            } else {
              System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
              bytecount += datasize;
            }

            Element filenode = doc.createElement("File");
            filenode.setAttribute("filename", current_dataname);
            filenode.setAttribute("channel", String.valueOf(ch));
            filenode.setAttribute("frame", String.valueOf(f));
            filenode.setAttribute("brickID", String.valueOf(i));
            filenode.setAttribute("offset", String.valueOf(offset));
            filenode.setAttribute("datasize", String.valueOf(datasize));
            filenode.setAttribute("filetype", String.valueOf(filetype));

            fsnode.appendChild(filenode);

            curbricknum++;
            IJ.showProgress((double) (curbricknum) / (double) (totalbricknum));
          }
          if (bytecount > 0) {
            BufferedOutputStream fis = null;
            try {
              File file = new File(directory + current_dataname);
              fis = new BufferedOutputStream(new FileOutputStream(file));
              fis.write(packed_data, 0, bytecount);
            } catch (IOException e) {
              e.printStackTrace();
              return;
            } finally {
              try {
                if (fis != null) fis.close();
              } catch (IOException e) {
                e.printStackTrace();
                return;
              }
            }
          }
        }
      }

      for (int i = 0; i < bricks.size(); i++) {
        Brick b = bricks.get(i);
        Element bricknode = doc.createElement("Brick");
        bricknode.setAttribute("id", String.valueOf(i));
        bricknode.setAttribute("st_x", String.valueOf(b.x_));
        bricknode.setAttribute("st_y", String.valueOf(b.y_));
        bricknode.setAttribute("st_z", String.valueOf(b.z_));
        bricknode.setAttribute("width", String.valueOf(b.w_));
        bricknode.setAttribute("height", String.valueOf(b.h_));
        bricknode.setAttribute("depth", String.valueOf(b.d_));
        brksnode.appendChild(bricknode);

        Element tboxnode = doc.createElement("tbox");
        tboxnode.setAttribute("x0", String.valueOf(b.tx0_));
        tboxnode.setAttribute("y0", String.valueOf(b.ty0_));
        tboxnode.setAttribute("z0", String.valueOf(b.tz0_));
        tboxnode.setAttribute("x1", String.valueOf(b.tx1_));
        tboxnode.setAttribute("y1", String.valueOf(b.ty1_));
        tboxnode.setAttribute("z1", String.valueOf(b.tz1_));
        bricknode.appendChild(tboxnode);

        Element bboxnode = doc.createElement("bbox");
        bboxnode.setAttribute("x0", String.valueOf(b.bx0_));
        bboxnode.setAttribute("y0", String.valueOf(b.by0_));
        bboxnode.setAttribute("z0", String.valueOf(b.bz0_));
        bboxnode.setAttribute("x1", String.valueOf(b.bx1_));
        bboxnode.setAttribute("y1", String.valueOf(b.by1_));
        bboxnode.setAttribute("z1", String.valueOf(b.bz1_));
        bricknode.appendChild(bboxnode);
      }

      if (l < lv - 1) {
        imp = WindowManager.getImage(lvImgTitle.get(l + 1));
        int[] newdims = imp.getDimensions();
        imageW = newdims[0];
        imageH = newdims[1];
        imageD = newdims[3];
        xspc = orgxspc * ((double) orgW / (double) imageW);
        yspc = orgyspc * ((double) orgH / (double) imageH);
        zspc = orgzspc * ((double) orgD / (double) imageD);
        bdepth = imp.getBitDepth();
      }
    }

    File newXMLfile = new File(directory + basename + ".vvd");
    writeXML(newXMLfile, doc);

    for (int l = 1; l < lv; l++) {
      imp = WindowManager.getImage(lvImgTitle.get(l));
      imp.changes = false;
      imp.close();
    }
  }
 void drawRoiFilledParticle(ImageProcessor ip, Roi roi, ImageProcessor mask, int count) {
   int grayLevel = (count < 65535) ? count : 65535;
   ip.setValue((double) grayLevel);
   ip.setRoi(roi.getBounds());
   ip.fill(mask);
 }
 void drawFilledParticle(ImageProcessor ip, Roi roi, ImageProcessor mask) {
   // IJ.write(roi.getBounds()+" "+mask.length);
   ip.setRoi(roi.getBounds());
   ip.fill(mask);
 }
 void analyzeParticle(int x, int y, ImagePlus imp, ImageProcessor ip) {
   // Wand wand = new Wand(ip);
   ImageProcessor ip2 = redirectIP != null ? redirectIP : ip;
   wand.autoOutline(x, y, level1, level2, wandMode);
   if (wand.npoints == 0) {
     IJ.log("wand error: " + x + " " + y);
     return;
   }
   Roi roi = new PolygonRoi(wand.xpoints, wand.ypoints, wand.npoints, roiType);
   Rectangle r = roi.getBounds();
   if (r.width > 1 && r.height > 1) {
     PolygonRoi proi = (PolygonRoi) roi;
     pf.setPolygon(proi.getXCoordinates(), proi.getYCoordinates(), proi.getNCoordinates());
     ip2.setMask(pf.getMask(r.width, r.height));
     if (floodFill) ff.particleAnalyzerFill(x, y, level1, level2, ip2.getMask(), r);
   }
   ip2.setRoi(r);
   ip.setValue(fillColor);
   ImageStatistics stats = getStatistics(ip2, measurements, calibration);
   boolean include = true;
   if (excludeEdgeParticles) {
     if (r.x == minX || r.y == minY || r.x + r.width == maxX || r.y + r.height == maxY)
       include = false;
     if (polygon != null) {
       Rectangle bounds = roi.getBounds();
       int x1 = bounds.x + wand.xpoints[wand.npoints - 1];
       int y1 = bounds.y + wand.ypoints[wand.npoints - 1];
       int x2, y2;
       for (int i = 0; i < wand.npoints; i++) {
         x2 = bounds.x + wand.xpoints[i];
         y2 = bounds.y + wand.ypoints[i];
         if (!polygon.contains(x2, y2)) {
           include = false;
           break;
         }
         if ((x1 == x2 && ip.getPixel(x1, y1 - 1) == fillColor)
             || (y1 == y2 && ip.getPixel(x1 - 1, y1) == fillColor)) {
           include = false;
           break;
         }
         x1 = x2;
         y1 = y2;
       }
     }
   }
   ImageProcessor mask = ip2.getMask();
   if (minCircularity > 0.0 || maxCircularity < 1.0) {
     double perimeter = roi.getLength();
     double circularity =
         perimeter == 0.0 ? 0.0 : 4.0 * Math.PI * (stats.pixelCount / (perimeter * perimeter));
     if (circularity > 1.0) circularity = 1.0;
     // IJ.log(circularity+"	"+perimeter+"  "+stats.area);
     if (circularity < minCircularity || circularity > maxCircularity) include = false;
   }
   if (stats.pixelCount >= minSize && stats.pixelCount <= maxSize && include) {
     particleCount++;
     if (roiNeedsImage) roi.setImage(imp);
     stats.xstart = x;
     stats.ystart = y;
     saveResults(stats, roi);
     if (showChoice != NOTHING) drawParticle(drawIP, roi, stats, mask);
   }
   if (redirectIP != null) ip.setRoi(r);
   ip.fill(mask);
 }
  void Otsu(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) {
    // Otsu's threshold algorithm
    // C++ code by Jordan Bevik <*****@*****.**>
    // ported to ImageJ plugin by G.Landini. Same algorithm as in Auto_Threshold, this time on local
    // circular regions
    int[] data;
    int w = imp.getWidth();
    int h = imp.getHeight();
    int position;
    int radiusx2 = radius * 2;
    ImageProcessor ip = imp.getProcessor();
    byte[] pixels = (byte[]) ip.getPixels();
    byte[] pixelsOut =
        new byte
            [pixels.length]; // need this to avoid changing the image data (and further histograms)
    byte object;
    byte backg;

    if (doIwhite) {
      object = (byte) 0xff;
      backg = (byte) 0;
    } else {
      object = (byte) 0;
      backg = (byte) 0xff;
    }

    int k, kStar; // k = the current threshold; kStar = optimal threshold
    int N1, N; // N1 = # points with intensity <=k; N = total number of points
    double BCV, BCVmax; // The current Between Class Variance and maximum BCV
    double num, denom; // temporary bookeeping
    int Sk; // The total intensity for all histogram points <=k
    int S,
        L =
            256; // The total intensity of the image. Need to hange here if modifying for >8 bits
                 // images
    int roiy;

    Roi roi = new OvalRoi(0, 0, radiusx2, radiusx2);
    // ip.setRoi(roi);
    for (int y = 0; y < h; y++) {
      IJ.showProgress(
          (double) (y) / (h - 1)); // this method is slow, so let's show the progress bar
      roiy = y - radius;
      for (int x = 0; x < w; x++) {
        roi.setLocation(x - radius, roiy);
        ip.setRoi(roi);
        // ip.setRoi(new OvalRoi(x-radius, roiy, radiusx2, radiusx2));
        position = x + y * w;
        data = ip.getHistogram();

        // Initialize values:
        S = N = 0;
        for (k = 0; k < L; k++) {
          S += k * data[k]; // Total histogram intensity
          N += data[k]; // Total number of data points
        }

        Sk = 0;
        N1 = data[0]; // The entry for zero intensity
        BCV = 0;
        BCVmax = 0;
        kStar = 0;

        // Look at each possible threshold value,
        // calculate the between-class variance, and decide if it's a max
        for (k = 1; k < L - 1; k++) { // No need to check endpoints k = 0 or k = L-1
          Sk += k * data[k];
          N1 += data[k];

          // The float casting here is to avoid compiler warning about loss of precision and
          // will prevent overflow in the case of large saturated images
          denom = (double) (N1) * (N - N1); // Maximum value of denom is (N^2)/4 =  approx. 3E10

          if (denom != 0) {
            // Float here is to avoid loss of precision when dividing
            num = ((double) N1 / N) * S - Sk; // Maximum value of num =  255*N = approx 8E7
            BCV = (num * num) / denom;
          } else BCV = 0;

          if (BCV >= BCVmax) { // Assign the best threshold found so far
            BCVmax = BCV;
            kStar = k;
          }
        }
        // kStar += 1;	// Use QTI convention that intensity -> 1 if intensity >= k
        // (the algorithm was developed for I-> 1 if I <= k.)
        // return kStar;
        pixelsOut[position] = ((int) (pixels[position] & 0xff) > kStar) ? object : backg;
      }
    }
    for (position = 0; position < w * h; position++)
      pixels[position] = pixelsOut[position]; // update with thresholded pixels
  }